It was from a Dropbox-like application (QSync client). It's not a problem with Dropbox as Dropbox always refuses to update the .db file until I close CintaNotes for a while (with the flip-side being it's a bit of a nuisance to update your notebook).

Yes "notebook.disconnect.enabled = 1" is in cintanotes.settings. Despite this, Dropbox hasn't worked for me for quite some time.

I think what is actually allowing QSync to replace the notebook out from under Cintanotes is the fact the notebook on one PC is stored and accessed via a Windows network SMB/CIFS share. Another error I have just got is

"class db::DatabaseException SQLite error 10: disk I/O error"

Which repeatedly pops up with only one button (OK), at least 30 or so times. I suspect this is either to do with the network share or QSync, I'm unsure. Either way, the notebook appears to be just fine.

Oh, network share is a whole different story that opens up a lot of possibilities for subtle bugs, so you need to be extra careful when using CN like that. Note that this is not officially supported, although seems to work most of the time. Better make sure there are a lot of regular backups done!